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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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TR and time_units do not match in pre-processed output #1725

Open cmpetty opened 5 years ago

cmpetty commented 5 years ago

Raw input data were 1000.00 msecs 

tesla:func cmp12$ fslhd ../../../../../ds001/sub-7564/ses-01/func/sub-7564_ses-01_task-reward_run-01_bold.nii.gz | egrep '(time_units|pixdim4)'
time_units  ms
pixdim4     1000.000000

preprocessed output was 1000.00 seconds 

tesla:func cmp12$ fslhd ../../../../fmriprep/sub-7564/ses-01/func/sub-7564_ses-01_task-reward_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz | egrep '(time_units|pixdim4)'
time_units  s
pixdim4     1000.000000
effigies commented 5 years ago

Thanks for this report... We should just override the TR with the JSON RepetitionTime metadata.

effigies commented 5 years ago

@cmpetty Would you be interested in contributing this fix? We'd be happy to help get you started.

cmpetty commented 5 years ago

@effigies i'm happy to contribute however i'm relatively new to the fmriprep environment. i noticed this when i tried to load up output data with Feat.